11-19210512-TG-T

Variant names:

• chr11-19210512-TG-T
• rs886048102
• ENST00000533783.2:c.-181delC

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The ENST00000533783.2(CSRP3):​c.-181delC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0039 (0 hom., cov: 15)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CSRP3 ENST00000533783.2 5_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:2
• Conservation: PhyloP100: -2.37

Genes affected

CSRP3 (HGNC:2472): (cysteine and glycine rich protein 3) This gene encodes a member of the CSRP family of LIM domain proteins, which may be involved in regulatory processes important for development and cellular differentiation. The LIM/double zinc-finger motif found in this protein is found in a group of proteins with critical functions in gene regulation, cell growth, and somatic differentiation. Mutations in this gene are thought to cause heritable forms of hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in humans. Alternatively spliced transcript variants with different 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Jul 2008]

CSRP3-AS1 (HGNC:54183): (CSRP3 and E2F8 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSRP3-AS1	NR_183675.1	n.207+13594delG		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSRP3	ENST00000533783.2	c.-181delC		5_prime_UTR_variant	Exon 1 of 7	1		ENSP00000431813.1
CSRP3-AS1	ENST00000527978.1	n.145+13594delG		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 413 AN: 104674 Hom.: 0 Cov.: 15 FAILED QC

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.00457

Gnomad AMR AF: 0.00613

Gnomad ASJ AF: 0.00328

Gnomad EAS AF: 0.00472

Gnomad SAS AF: 0.00896

Gnomad FIN AF: 0.00768

Gnomad MID AF: 0.00521

Gnomad NFE AF: 0.00411

Gnomad OTH AF: 0.00573

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 80 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 60

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00394 AC: 413 AN: 104752 Hom.: 0 Cov.: 15 AF XY: 0.00415 AC XY: 209 AN XY: 50352

Gnomad4 AFR AF: 0.00175

Gnomad4 AMR AF: 0.00622

Gnomad4 ASJ AF: 0.00328

Gnomad4 EAS AF: 0.00473

Gnomad4 SAS AF: 0.00870

Gnomad4 FIN AF: 0.00768

Gnomad4 NFE AF: 0.00411

Gnomad4 OTH AF: 0.00566

Alfa AF: 0.000601 Hom.: 0

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

Submissions by phenotype

Dilated Cardiomyopathy, Dominant Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypertrophic cardiomyopathy Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs886048102; hg19: chr11-19232059;